Friday, August 28, 2020

PRC ASBM Test in South China Sea


This is an interesting discussion of PRC Anti-Ship Ballistic Missiles (ASBM), including the DF21, DF26, and DF17 systems. You can set the captions to English if necessary. (Google realtime speech to text and translation have improved significantly in the last year or so.)

In response to US activity in the South China Sea and elsewhere, PRC recently conducted a test of DF21 and DF26 in the open ocean. Reportedly, a US "Cobra Ball" RC135S missile intelligence aircraft was present to monitor the activity. 

The YouTube video discusses PRC ASBM capabilities, including 

1. Infrared and radar final targeting
2. Maneuver capability
3. Capability of the missile to receive (ground based) over-the-horizon radar and satellite information while in flight. 

These are the frequent subject of speculation in Western sources: "There is a long kill chain and we are not sure whether it is operational..." etc.

Assuming that PRC ASBM have these capabilities, which seems quite plausible to me, this test was presumably a demonstration for the US, to make sure that our military appreciates the PLARF ability to hit a moving target (e.g., US aircraft carrier) at sea. Once this mutual understanding is in place, FONOPs in the South China Sea become mere theatrics for the dim witted.

See related posts

The Future of the U.S. Aircraft Carrier: Fearsome Warship or Expensive Target? (Heritage panel; video) 

Machine intelligence threatens overpriced aircraft carriers (first principles analysis of final targeting problem)

A2AD fait accompli? (Yaogan satellite surveillance of the western Pacific)

Tuesday, August 25, 2020

The Inheritors and The Grisly Folk: H.G. Wells and William Golding on Neanderthals

Some time ago I posted about The Grisly Folk by H.G. Wells, an essay on Neanderthals and their encounters with modern humans. See also The Neanderthal Problem, about the potential resurrection of early hominids via genomic technology, and the associated ethical problems. 

The Grisly Folk: ... Many and obstinate were the duels and battles these two sorts of men fought for this world in that bleak age of the windy steppes, thirty or forty thousand years ago. The two races were intolerable to each other. They both wanted the eaves and the banks by the rivers where the big flints were got. They fought over the dead mammoths that had been bogged in the marshes, and over the reindeer stags that had been killed in the rutting season. When a human tribe found signs of the grisly folk near their cave and squatting place, they had perforce to track them down and kill them; their own safety and the safety of their little ones was only to be secured by that killing. The Neandertalers thought the little children of men fair game and pleasant eating. ...

William Golding was inspired by Wells to write The Inheritors (his second book, after Lord of the Flies), which is rendered mostly (until the end, at which point the perspective is reversed) from the Neanderthal point of view. Both Wells and Golding assume that Neanderthals were not as cognitively capable as modern humans, but Golding's primitives are peaceful quasi-vegetarians, quite unlike the Grisly Folk of Wells.

The Inheritors 
Golding considered this his finest novel and it is a beautifully realised tale about the last days of the Neanderthal people and our fear of the ‘other’ and the unfamiliar. The action is revealed through the eyes of the Neanderthals whose peaceful world is threatened by the emergence of Homo sapiens. 
The struggle between the simple Neanderthals and the malevolent modern humans ends in helpless despair ... 
From the book jacket: "When the spring came the people - what was left of them - moved back by the old paths from the sea. But this year strange things were happening, terrifying things that had never happened before. Inexplicable sounds and smells; new, unimaginable creatures half glimpsed through the leaves. What the people didn't, and perhaps never would, know, was that the day of their people was already over."

See this episode of the podcast Backlisted for an excellent discussion of the book. 

I am particularly interested in how Golding captures the perspective of pre-humans with limited cognitive abilities. He conveys the strangeness and incomprehensibility of modern humans as perceived by Neanderthals. In this sense, the book is a type of Science Fiction: it describes a first encounter with Aliens of superior capability.

We are approaching the day when modern humans will encounter a new and quasi-alien intelligence: it may be AI, or it may be genetically enhanced versions of ourselves.

On a scientific note, can someone provide an update to this 2013 work: "... high quality genome sequence obtained from the toe of a female Neanderthal who lived in the Altai mountains in Siberia. Interestingly, copy number variation at 16p11.2 is one of the structural variants identified in a recent deCODE study as related to IQ depression"? Here is an interesting follow up paper: Nature 2016 Aug 11; 536(7615): 205–209.



Saturday, August 15, 2020

Othram identifies murder victim from ~20 cells equivalent DNA sample

Othram, a DNA forensics company I co-founded, continues to solve cold cases around the world. 

Murder victim Rodney Peter Johnson was identified from a sample of only 0.2 nanograms of DNA (equivalent of 20 cells). Mr. Johnson had last been seen in 1987, when he was 25 years old. His body was discovered in 1994 by a fisherman in Lake Stickney, near Everett WA. It was badly decomposed and could not be identified.

The Johnson family has waited decades for closure. Press conference video.

See Othram: the future of DNA forensics

The existing FBI standard (CODIS) for DNA identification uses only 20 markers (STRs -- previously only 13 loci were used!). By contrast, genome wide sequencing can reliably call millions of genetic variants. 

For the first time, the cost curves for these two methods have crossed: modern sequencing costs no more than extracting CODIS markers using the now ~30 year old technology. 

What can you do with millions of genetic markers? 

1. Determine relatedness of two individuals with high precision. This allows detectives to immediately identify a relative (ranging from distant cousin to sibling or parent) of the source of the DNA sample, simply by scanning through large DNA databases. ...

If you have contacts in law enforcement, please alert them to the potential of this new technology.

Cheap Document Camera

I built this using a $35 1080p web camera and a $20 LED lamp I already had in my office. 

I've tested on Google Meet and Zoom, it allows me to display equations and quick sketches to collaborators and students. There are much fancier purpose-built document cameras with similar functionality, but these are mostly sold out on Amazon, due to the increase in remote work and online teaching. The particular web cam I am using (see link above) has a manual focus, in case the software auto-focus is unsatisfactory.

Both Google Meet and Zoom allow to switch from the default internal camera on my laptop to the external web cam (a simple toggle in Settings). The web cam is auto-detected on both Mac OS and Chrome -- I did not have to install any drivers.

The plastic clip I used to attach the web cam to the lamp is from the kitchen (Bed Bath and Beyond). Tape would also work as the web cam is very light.

Here is the rig in action, using Google Meet. I write on the pad and my colleague can see it very clearly.

Wednesday, August 12, 2020

U.S.-China Decoupling: Separating Myth From Reality (Georgetown panel)


This is a good panel on US-China decoupling, from June 2020. I especially recommend the discussion between 1h and 1h30m.

Regarding semiconductors: How fast will SMIC close the gap with TSMC? It's now a huge priority. 

Chip design in China advanced much faster than most US observers expected in the past few years, and I think semiconductor fabrication will also advance quickly in the future. Fabs are huge, complex infrastructure investments, which they tend to do well. (According to Goodrich, 60 fabs under construction right now in China.) I also expect them to be good at fine-tuning the production process, pulling in engineering talent from Taiwan and S. Korea as necessary. The most difficult technology hurdle will be the advanced lithography machines that still depend on US and European intellectual property. 
Georgetown US-China Dialogue 2020 
Wang Tao is a managing director and head of Asia Economic Research at UBS investment bank in Hong Kong. She covers macroeconomic and policy issues in Asia and China. 
Jörg Wuttke is the chief representative in China of BASF, a large German chemical company. He is also the president of the European Union Chamber of Commerce in China. 
Dan Wang is a Beijing-based technology analyst at Gavekal Dragonomics, an economic research firm. His focus is on China's technology progress—especially on semiconductors—as well as the unfolding tech war related to the Committee on Foreign Investment in the United States, export controls, and Huawei. 
Jimmy Goodrich is vice president for global policy at the Semiconductor Industry Association (SIA). In this role, he leads SIA’s global policy team and its research and analysis of foreign semiconductor policies and capabilities. Jimmy is also the executive committee chair of the United States Information Technology Office (USITO) in Beijing, representing SIA in his capacity.

Related: China's eRMB, a blockchain based digital currency linked 1-1 to the yuan, seems to be flying under the radar. In my opinion this has huge possibilities -- in the future, anyone with the app (an eRMB account) can transact in RMB whether they are in Germany or Iran. This development is an inevitable consequence of the US weaponizing SWIFT...  

Ray Dalio Warns of U.S.-China ‘Capital War’ That Would Hit Dollar (Bloomberg)


Thursday, August 06, 2020

Sibling Validation of Polygenic Risk Scores and Complex Trait Prediction (Nature Scientific Reports)

This is the published version of our paper which uses tens of thousands of siblings to validate polygenic trait and risk prediction. We show that the predictors can differentiate between siblings (which one has heart disease? is taller?), despite similarity in childhood environments and genotype. The predictors work almost as well in pairwise sibling comparisons as in comparisons between randomly selected strangers. 

There are now many validations of polygenic prediction in the scientific literature, conducted using groups of people born on different continents and in different decades than the original populations used in training. With the new sibling results our confidence is extremely high that the predictors are capturing causal genetic effects, and that complex trait prediction from DNA alone is a reality.
Sibling Validation of Polygenic Risk Scores and Complex Trait Prediction 

Louis Lello, Timothy Raben, Stephen D. H. Hsu
I posted about the bioRxiv preprint version back in March:
We test a variety of polygenic predictors using tens of thousands of genetic siblings for whom we have SNP genotypes, health status, and phenotype information in late adulthood. Siblings have typically experienced similar environments during childhood, and exhibit negligible population stratification relative to each other. Therefore, the ability to predict differences in disease risk or complex trait values between siblings is a strong test of genomic prediction in humans. We compare validation results obtained using non-sibling subjects to those obtained among siblings and find that typically most of the predictive power persists in within-family designs. In the case of disease risk we test the extent to which higher polygenic risk score (PRS) identifies the affected sibling, and also compute Relative Risk Reduction as a function of risk score threshold. For quantitative traits we examine between-sibling differences in trait values as a function of predicted differences, and compare to performance in non-sibling pairs. Example results: Given 1 sibling with normal-range PRS score (less than 84th percentile) and 1 sibling with high PRS score (top few percentiles), the predictors identify the affected sibling about 70-90 percent of the time across a variety of disease conditions, including Breast Cancer, Heart Attack, Diabetes, etc. For height, the predictor correctly identifies the taller sibling roughly 80 percent of the time when the (male) height difference is 2 inches or more.

From the paper:
If a girl grows up to be taller than her sister, with whom she spent the first 18 years of her life, it seems likely at least some of the height difference is due to genetic differences. How much of phenotype difference can we predict from DNA alone? If one of the sisters develops breast cancer later in life, how much of the risk was due to genetic variants that she does not share with her asymptomatic sister? These are fundamental questions in human biology, which we address (at least to some extent) in this paper.

... We emphasize that predictors trained on even larger datasets will likely have significantly stronger performance than the ones analyzed here [13, 14]. As we elaborated in earlier work, where many of these predictors were first investigated, their main practical utility at the moment is in the identification of outliers who may be at exceptionally high (or low) risk for a specific disease condition. The results here confirm that high risk score outliers are indeed at elevated risk, even compared to their (normal range score) siblings.

The sibling results presented in this paper, together with the many out of sample validations of polygenic scores that continue to appear in the literature, suggest that genomic prediction in humans is a robust and important advance that will lead to improvements in translational medicine as well as deep insights into human genetics.

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